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- PDB-2jrh: Solution structure of human MEKK3 PB1 domain cis isomer -

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Basic information

Entry
Database: PDB / ID: 2jrh
TitleSolution structure of human MEKK3 PB1 domain cis isomer
ComponentsMitogen-activated protein kinase kinase kinase 3
KeywordsTRANSFERASE / kinase signaling domain
Function / homology
Function and homology information


positive regulation of cell proliferation in bone marrow / mitogen-activated protein kinase kinase kinase / positive regulation of p38MAPK cascade / positive regulation of cell migration involved in sprouting angiogenesis / blood vessel development / negative regulation of cellular senescence / MAP kinase kinase kinase activity / Interleukin-1 signaling / MAPK cascade / positive regulation of canonical NF-kappaB signal transduction ...positive regulation of cell proliferation in bone marrow / mitogen-activated protein kinase kinase kinase / positive regulation of p38MAPK cascade / positive regulation of cell migration involved in sprouting angiogenesis / blood vessel development / negative regulation of cellular senescence / MAP kinase kinase kinase activity / Interleukin-1 signaling / MAPK cascade / positive regulation of canonical NF-kappaB signal transduction / protein autophosphorylation / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll ...Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Model detailsMitogen Activated Protein Kinase Kinase Kinase 3 PB1 domain (Residues 42-126) cis isomer
AuthorsQi, H. / Jiahai, Z. / Jihui, W. / Yunyu, S.
CitationJournal: Biochemistry / Year: 2007
Title: Insight into the Binding Properties of MEKK3 PB1 to MEK5 PB1 from Its Solution Structure.
Authors: Hu, Q. / Shen, W. / Huang, H. / Liu, J. / Zhang, J. / Huang, X. / Wu, J. / Shi, Y.
History
DepositionJun 26, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 3


Theoretical massNumber of molelcules
Total (without water)11,1871
Polymers11,1871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 3 / MAPK/ERK kinase kinase 3 / MEK kinase 3 / MEKK 3


Mass: 11186.697 Da / Num. of mol.: 1 / Fragment: OPR, PB1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K3, MAPKKK3, MEKK3 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q99759, mitogen-activated protein kinase kinase kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Mitogen Activated Protein Kinase Kinase Kinase 3 PB1 domain (Residues 42-126) cis isomer
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HBHA(CO)NH
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D (H)CCH-COSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11122D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] MEKK3 PB1-cis, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 15N] MEKK3 PB1-cis, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMEKK3 PB1-cis[U-100% 13C; U-100% 15N]1
0.8 mMMEKK3 PB1-cis[U-100% 15N]2
Sample conditionspH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readdata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readprocessing
MOLMOLKoradi, Billeter and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
MOLMOLKoradi, Billeter and Wuthrichprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: The structures are based on a total of 1296 restraints, 1156 are noe-derived distance constraints, 112 dihedral angle restraints,28 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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